powerlecture: chapter 16 studying and manipulating genomes
TRANSCRIPT
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PowerLecture:PowerLecture:Chapter 16Chapter 16
Studying and Manipulating Studying and Manipulating GenomesGenomes
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Fig. 16-1a, p.242
Golden Rice, or Frankenfood?Golden Rice, or Frankenfood?
Ordinary daffodil
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124 million children around the world have 124 million children around the world have vitamin A deficienciesvitamin A deficiencies
Golden rice Golden rice ––Rice plants engineered with genes from daffodils Rice plants engineered with genes from daffodils
allowing it to produce beta-carotine in its seeds allowing it to produce beta-carotine in its seeds (rice) (rice)
––Beta carotine is the precursor to Vitamin ABeta carotine is the precursor to Vitamin A
Rice is the main food for 3 billion peopleRice is the main food for 3 billion people
Impacts, Issues: Impacts, Issues: Golden Rice, or Golden Rice, or Frankenfood?Frankenfood?
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Fig. 16-1b, p.242
Golden Rice, or Frankenfood?Golden Rice, or Frankenfood?
Regular rice
1st generation2nd generation
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Many crops plants have been modified, Many crops plants have been modified, including corn, beets, potatoes, and cottonincluding corn, beets, potatoes, and cotton
Potentially less harmful to the environment Potentially less harmful to the environment than current agricultural practicesthan current agricultural practices
Impacts, Issues: Impacts, Issues: Golden Rice, or Golden Rice, or Frankenfood?Frankenfood?
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p.243
Golden Rice, or Frankenfood?Golden Rice, or Frankenfood?
Today's cornAncestral corn
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Discovery of Restriction Discovery of Restriction EnzymesEnzymes
Hamilton Smith was studying how Hamilton Smith was studying how Haemophilus influenzaeHaemophilus influenzae defend defend themselves from bacteriophage attackthemselves from bacteriophage attack
Discovered bacteria have an enzyme that Discovered bacteria have an enzyme that chops up viral DNA chops up viral DNA
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Specificity of CutsSpecificity of Cuts
Restriction enzymes cut DNA at a Restriction enzymes cut DNA at a specific sequencespecific sequence
Number of cuts made in DNA will Number of cuts made in DNA will depend on number of times the “target” depend on number of times the “target” sequence occurssequence occurs
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3’
5’ 3’
5’GC T T A A
A A T T C
G
another DNA fragment
5’
3’
G
one DNA fragment
3’
5’C T T A A
A A T T C
nick
nick
G A A T T C
GC T T A A3’
5’ 3’
5’
DNA ligase action
GC T T A A3’
5’ 3’
5’
A A T T CG
Fig. 16-2, p.244
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TermsTerms
DNA ligase – seals cuts in DNADNA ligase – seals cuts in DNA Recombinant DNA – any molecule Recombinant DNA – any molecule
consisting of base sequences from 2 or consisting of base sequences from 2 or more organisms of the same or different more organisms of the same or different speciesspecies
Cloning vector – a plasmid that has Cloning vector – a plasmid that has accepted foreign DNA and can be slipped accepted foreign DNA and can be slipped into hostinto host
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Using PlasmidsUsing Plasmids
Plasmid is small circle of Plasmid is small circle of
bacterial DNAbacterial DNA
Foreign DNA can be inserted Foreign DNA can be inserted
into plasmidinto plasmid
Forms recombinant plasmidsForms recombinant plasmids
Plasmid is a cloning vectorPlasmid is a cloning vector
Can deliver DNA into another cellCan deliver DNA into another cell
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Fig. 16-3a, p.244
PlasmidsPlasmids
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a A restriction enzymecuts a specific base sequence everywhere it occurs in DNA.
c The same enzyme cuts the same sequnece in plasmid DNA.
d The plasmid DNA also has sticky ends
e The DNA fragments and the plasmid DNA are mixed with DNA ligase.
f The result? A collection of recombinant plasmids that incorporate foreign DNA fragments.
g Host cells that can divide rapidly take up the recombinant plasmids.
b The DNA fragmentshave sticky ends.
Fig. 16-4, p.245
Using Plasmids
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Making cDNAMaking cDNA
Fig. 16-5, p.245
•Use reverse transcriptase onto one strand of complementary DNA (cDNA)•DNA polymerase strips RNA bases•Copies cDNA into a second strand
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Gene LibrariesGene Libraries
Bacteria that contain different Bacteria that contain different
cloned DNA fragmentscloned DNA fragments
Genomic libraryGenomic library
cDNA librarycDNA library
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Use of a ProbeUse of a Probe Colonies on plate
Cells adhere to filter
Cells are lysed;DNA sticks to filter
Probe is added
Location where probe binds forms dark spot on film, indicates colony with gene
You want to find You want to find
which bacteria in a which bacteria in a
library contain a library contain a
specific genespecific gene
Need a probe for that Need a probe for that
genegene
• A radioisotope-A radioisotope-
labeled piece of labeled piece of
DNADNA
• Will base-pair with Will base-pair with
gene of interestgene of interest
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Making a ProbeMaking a Probe
Make a primer if the sequence is known.Make a primer if the sequence is known. If not usually DNA from closely related speciesIf not usually DNA from closely related species
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Amplifying DNAAmplifying DNA
Fragments can be inserted into Fragments can be inserted into fast-growing microorganisms fast-growing microorganisms
Polymerase chain reaction (PCR) Polymerase chain reaction (PCR)
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Polymerase Chain ReactionPolymerase Chain Reaction
Sequence to be copied is heatedSequence to be copied is heated Primers are added and bind to ends of Primers are added and bind to ends of
single strandssingle strands DNA polymerase uses free nucleotides DNA polymerase uses free nucleotides
to create complementary strandsto create complementary strands Doubles number of copies of DNADoubles number of copies of DNA Animation
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Polymerase Polymerase Chain ReactionChain Reaction
Double-stranded DNA to copy
DNA heated to 90°– 94°C
Primers added to base-pair with ends
Mixture cooled; base-pairing of primers and ends of DNA strands
DNA polymerasesassemble new DNA strands
Fig. 16-6, p. 256
Stepped Art
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Polymerase Polymerase Chain ReactionChain Reaction
Stepped Art
Mixture heated again; makes all DNA fragments unwind
Mixture cooled; base-pairing between primers and ends of single DNA strands
DNA polymerase action again doubles number of identical DNA fragments
Fig. 16-6, p. 256
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Recording Recording the the Sequence Sequence
T C C A T G G A C CT C C A T G G A C
T C C A T G G A
T C C A T G G
T C C A T G
T C C A T
T C C A
T C C
T C
T
electrophoresisgel
one of the many fragments of DNA migratingthrough the gel
one of the DNA fragmentspassing through a laser beam after moving through the gel
T C C A T G G A C C A
•DNA is placed on gel
•Fragments move off
gel in size order; pass
through laser beam
•Color each fragment
fluoresces is recorded
on printout
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Fig. 16-8b, p.248
Recording the Sequence
http://www.dnalc.org/ddnalc/resources/cycseq.html
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Genome SequencingGenome Sequencing
1995 - Sequence of bacterium 1995 - Sequence of bacterium Haemophilus influenzaeHaemophilus influenzae determined determined
Automated DNA sequencing now main Automated DNA sequencing now main methodmethod
Draft sequence of entire human genome Draft sequence of entire human genome determined in this waydetermined in this way
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Fig. 16-10a, p.250
Genome SequencingGenome Sequencing
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Nucleotides for SequencingNucleotides for Sequencing
Standard nucleotides (A, T, C, G)Standard nucleotides (A, T, C, G) Modified versions of these nucleotides Modified versions of these nucleotides
Labeled so they fluoresceLabeled so they fluoresce Structurally different so that they stop DNA Structurally different so that they stop DNA
synthesis when they are added to a strandsynthesis when they are added to a strand
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Reaction MixtureReaction Mixture
Copies of DNA to be sequencedCopies of DNA to be sequenced PrimerPrimer DNA polymeraseDNA polymerase Standard nucleotidesStandard nucleotides Modified nucleotidesModified nucleotides
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DNA FingerprintsDNA Fingerprints
Unique array of DNA fragmentsUnique array of DNA fragments
Inherited from parents in Mendelian Inherited from parents in Mendelian
fashionfashion
Even full siblings can be distinguished Even full siblings can be distinguished
from one another by this technique from one another by this technique
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Tandem RepeatsTandem Repeats
Short regions of DNA that differ Short regions of DNA that differ substantially among peoplesubstantially among people
Many sites in genome where tandem Many sites in genome where tandem repeats occurrepeats occur
Each person carries a unique Each person carries a unique combination of repeat numberscombination of repeat numbers
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RFLPsRFLPs
Restriction fragment length polymorphismsRestriction fragment length polymorphisms DNA from areas with tandem repeats is cut DNA from areas with tandem repeats is cut
with restriction enzymeswith restriction enzymes Because of the variation in the amount of Because of the variation in the amount of
repeated DNA, the restriction fragments repeated DNA, the restriction fragments vary in sizevary in size
Variation is detected by gel electrophoresisVariation is detected by gel electrophoresis
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Gel ElectrophoresisGel Electrophoresis
DNA is placed at one end of a gelDNA is placed at one end of a gel A current is applied to the gelA current is applied to the gel DNA molecules are negatively charged DNA molecules are negatively charged
and move toward positive end of geland move toward positive end of gel Smaller molecules move faster than larger Smaller molecules move faster than larger
onesones http://www.dnalc.org/ddnalc/resources/elec
trophoresis.html
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Fig. 16-9b, p.249
Gel Gel ElectrophoresisElectrophoresis
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Analyzing DNA Fingerprints Analyzing DNA Fingerprints
DNA is stained or made visible by use DNA is stained or made visible by use
of a radioactive probeof a radioactive probe
Pattern of bands is used to: Pattern of bands is used to:
Identify or rule out criminal suspectsIdentify or rule out criminal suspects
Identify bodiesIdentify bodies
Determine paternityDetermine paternity
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GenomicsGenomics
Structural genomics: actual mapping and Structural genomics: actual mapping and sequencing of genomes of individuals sequencing of genomes of individuals
Comparative genomics: concerned with Comparative genomics: concerned with possible evolutionary relationships of possible evolutionary relationships of groups of organismsgroups of organisms
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Reactions ProceedReactions Proceed
Nucleotides are assembled to create Nucleotides are assembled to create complementary strandscomplementary strands
When a modified nucleotide is included, When a modified nucleotide is included, synthesis stopssynthesis stops
Result is millions of tagged copies of Result is millions of tagged copies of varying lengthvarying length
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DNA ChipsDNA Chips
Microarrays of Microarrays of thousands of gene thousands of gene sequences sequences representing a large representing a large subset of an entire subset of an entire genome (p251)genome (p251)
Stamped onto a glass Stamped onto a glass plate the size of a plate the size of a small business card small business card (p251)(p251)
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Genetic EngineeringGenetic Engineering
Genes are isolated, modified, and inserted Genes are isolated, modified, and inserted into an organisminto an organism
Made possible by recombinant technologyMade possible by recombinant technology
Cut DNA up and recombine piecesCut DNA up and recombine pieces
Amplify modified pieces Amplify modified pieces
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Engineered ProteinsEngineered Proteins
Bacteria can be used to grow medically Bacteria can be used to grow medically
valuable proteinsvaluable proteins
Insulin, interferon, blood-clotting factorsInsulin, interferon, blood-clotting factors
VaccinesVaccines
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Cleaning Up the EnvironmentCleaning Up the Environment
Microorganisms normally break down Microorganisms normally break down
organic wastes and cycle materialsorganic wastes and cycle materials
Some can be engineered to break down Some can be engineered to break down
pollutants or to take up larger amounts pollutants or to take up larger amounts
of harmful materialsof harmful materials
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Can Genetically Engineered Can Genetically Engineered Bacteria “Escape”?Bacteria “Escape”?
Genetically engineered bacteria are Genetically engineered bacteria are designed so that they cannot survive designed so that they cannot survive outside laboutside lab
Genes are included that will be turned Genes are included that will be turned on in outside environment, triggering on in outside environment, triggering deathdeath
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p.252
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Engineered PlantsEngineered Plants
Cotton plants that display resistance to Cotton plants that display resistance to herbicideherbicide
Aspen plants that produce less lignin and Aspen plants that produce less lignin and more cellulosemore cellulose
Tobacco plants that produce human Tobacco plants that produce human proteinsproteins
Mustard plant cells that produce Mustard plant cells that produce biodegradable plasticbiodegradable plastic
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Fig. 16-12a, p.253
Engineered Plants
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Fig. 16-12b, p.253
Engineered Plants
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The Ti plasmidThe Ti plasmid
Researchers Researchers replace tumor-replace tumor-causing genes causing genes with beneficial with beneficial genes genes
Plasmid Plasmid transfers these transfers these genes to genes to cultured plant cultured plant cellscells
foreign genein plasmid
plant cell
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Fig. 16-13, p.253
a A bacterial cell contains a Ti plasmid (purple) that has a foreign gene (blue).
b The bacterium infects a plant and transfers the Ti plasmid into it.
c The plant cell divides.
d Transgenic plants.
e Young plants with a fluorescent gene product.
The Ti plasmid
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Genetic ChangesGenetic Changes
Humans have been changing the Humans have been changing the
genetics of other species for thousands genetics of other species for thousands
of yearsof years Artificial selection of plants and animalsArtificial selection of plants and animals
Natural processes also at workNatural processes also at work Mutation, crossing overMutation, crossing over
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First Engineered MammalsFirst Engineered Mammals
Experimenters used mice with hormone Experimenters used mice with hormone deficiency that leads to dwarfism deficiency that leads to dwarfism
Fertilized mouse eggs were injected Fertilized mouse eggs were injected with gene for rat growth hormone with gene for rat growth hormone
Gene was integrated into mouse DNAGene was integrated into mouse DNA Engineered mice were 1-1/2 times Engineered mice were 1-1/2 times
larger than unmodified littermateslarger than unmodified littermates
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Transgenic MiceTransgenic Mice
Fig. 16-15, p.254
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Designer CattleDesigner Cattle
Genetically identical cattle embryos can be Genetically identical cattle embryos can be grown in culturegrown in culture
Embryos can be genetically modifiedEmbryos can be genetically modified create resistance to mad cow diseasecreate resistance to mad cow disease engineer cattle to produce human serum engineer cattle to produce human serum
albumin for medical usealbumin for medical use
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Fig. 16-14a, p.254
Genetically Modified Animals
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Fig. 16-14b, p.254
Genetically Modified Animals
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Fig. 16-14c, p.254
Genetically Modified Animals
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XenotransplantationXenotransplantation
Researchers knockout the Ggta1genes in Researchers knockout the Ggta1genes in transgenic pigletstransgenic piglets
Ggta1 gene produces proteins that human Ggta1 gene produces proteins that human antibodies recognizeantibodies recognize
Pig’s organs are less prone to rejection by Pig’s organs are less prone to rejection by a humana human
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SafetySafety
SuperpathogensSuperpathogens DNA from pathogenic or toxic organisms DNA from pathogenic or toxic organisms
used in recombination experimentsused in recombination experiments Hok genesHok genes NIH guidelines for DNA researchNIH guidelines for DNA research
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The Human Genome InitiativeThe Human Genome Initiative
Goal - Map the entire human genomeGoal - Map the entire human genome Initially thought by many to be a waste of Initially thought by many to be a waste of
resourcesresources Process accelerated when Craig Ventner Process accelerated when Craig Ventner
used bits of cDNAs as hooks to find genesused bits of cDNAs as hooks to find genes Sequencing was completed ahead of Sequencing was completed ahead of
schedule in early 2001schedule in early 2001
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Results of Gene TherapyResults of Gene Therapy
Modified cells alive in woman’s liverModified cells alive in woman’s liver
Blood levels of LDLs down 20 percentBlood levels of LDLs down 20 percent
No evidence of atherosclerosis No evidence of atherosclerosis
Cholesterol levels remain highCholesterol levels remain high
Remains to be seen whether procedure will Remains to be seen whether procedure will
prolong her lifeprolong her life
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Using Human GenesUsing Human Genes
Even with gene in hand it is difficult to Even with gene in hand it is difficult to manipulate it to advantagemanipulate it to advantage
Viruses usually used to insert genes Viruses usually used to insert genes into cultured human cells but procedure into cultured human cells but procedure has problemshas problems
Very difficult to get modified genes to Very difficult to get modified genes to work where they shouldwork where they should
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Ethical IssuesEthical Issues
Who decides what should be Who decides what should be
“corrected” through genetic “corrected” through genetic
engineering?engineering?
Should animals be modified to provide Should animals be modified to provide
organs for human transplants?organs for human transplants?
Should humans be cloned?Should humans be cloned?